Strain identifier
BacDive ID: 132079
Type strain:
Species: Actinobaculum massiliense
Strain Designation: FC1, FC3
Strain history: <- S. Khelaifia, Timone Hospital, Marseille, France; FC3 <- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes
NCBI tax ID(s): 202789 (species)
General
@ref: 23870
BacDive-ID: 132079
DSM-Number: 100580
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, coccus-shaped, colony-forming
description: Actinobaculum massiliense FC1 is an anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from urine, 12-year-old patient with acute cystitis.
NCBI tax id
- NCBI tax id: 202789
- Matching level: species
strain history
- @ref: 23870
- history: <- S. Khelaifia, Timone Hospital, Marseille, France; FC3 <- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes
doi: 10.13145/bacdive132079.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Actinomycetales
- family: Actinomycetaceae
- genus: Actinobaculum
- species: Actinobaculum massiliense
- full scientific name: Actinobaculum massiliense corrig. Greub and Raoult 2002
synonyms
- @ref: 20215
- synonym: Actinobaculum massiliae
@ref: 23870
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Actinomycetaceae
genus: Actinobaculum
species: Actinobaculum massiliense
full scientific name: Actinobaculum massiliense Greub and Raoult 2006
strain designation: FC1, FC3
type strain: yes
Morphology
cell morphology
- @ref: 43943
- gram stain: positive
- cell shape: coccus-shaped
- motility: no
colony morphology
- @ref: 43943
- type of hemolysis: alpha
- hemolysis ability: 1
- colony size: 0.5-1.5 mm
- colony color: pale-grey
- colony shape: circular
- incubation period: 3 days
- medium used: Columbia agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
23870 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water |
43943 | Columbia agar | yes | 5% blood enriched |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
23870 | positive | growth | 37 | mesophilic |
43943 | positive | optimum | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
43943 | anaerobe |
43943 | microaerophile |
spore formation
- @ref: 43943
- spore formation: no
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43943 | 29864 | mannitol | - | builds acid from |
43943 | 37684 | mannose | - | builds acid from |
43943 | 16634 | raffinose | - | builds acid from |
43943 | 30911 | sorbitol | - | builds acid from |
43943 | 28017 | starch | - | builds acid from |
43943 | 27082 | trehalose | - | builds acid from |
43943 | 4853 | esculin | - | hydrolysis |
43943 | 5291 | gelatin | - | hydrolysis |
43943 | 17632 | nitrate | - | reduction |
43943 | 17234 | glucose | + | builds acid from |
43943 | 17306 | maltose | + | builds acid from |
43943 | 33942 | ribose | + | builds acid from |
43943 | 18222 | xylose | + | builds acid from |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | group ID | is resistant |
---|---|---|---|---|---|---|
43943 | 2676 | amoxicillin | yes | yes | ||
43943 | amoxicillin | yes | yes | 10 | ||
43943 | 48947 | clavulanic acid | yes | yes | 10 | |
43943 | 204928 | cefotaxime | yes | yes | ||
43943 | 29007 | ceftriaxone | yes | yes | ||
43943 | 471744 | imipenem | yes | yes | ||
43943 | 45924 | trimethoprim | yes | yes | 26 | |
43943 | 9332 | sulfamethoxazole | yes | yes | 26 | |
43943 | 48923 | erythromycin | yes | yes | ||
43943 | 50845 | doxycycline | yes | yes | ||
43943 | 28001 | vancomycin | yes | yes | ||
43943 | 28915 | fosfomycin | yes | yes | ||
43943 | 28077 | rifampicin | yes | yes | ||
43943 | 17833 | gentamicin | yes | yes | ||
43943 | 100241 | ciprofloxacin | yes | yes | ||
43943 | 37943 | colistin | yes | yes |
metabolite production
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
43943 | catalase | - | 1.11.1.6 |
43943 | cytochrome oxidase | - | 1.9.3.1 |
43943 | leucine arylamidase | + | 3.4.11.1 |
43943 | alpha-glucosidase | + | 3.2.1.20 |
43943 | beta-glucuronidase | + | 3.2.1.31 |
43943 | pyrazinamidase | +/- | 3.5.1.B15 |
43943 | beta-galactosidase | +/- | 3.2.1.23 |
43943 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
43943 | alkaline phosphatase | - | 3.1.3.1 |
43943 | urease | - | 3.5.1.5 |
43943 | alpha-galactosidase | - | 3.2.1.22 |
43943 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | serine arylamidase | + | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | + | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | + | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | + | 3.4.11.1 |
68380 | phenylalanine arylamidase | + | |
68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
68380 | proline-arylamidase | + | 3.4.11.5 |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
23870 | - | - | - | +/- | - | + | - | - | +/- | - | - | - | - | - | - | - | - | +/- | + | + | + | + | - | + | + | + | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | sampling date |
---|---|---|---|---|---|
23870 | urine, 12-year-old patient with acute cystitis | France | FRA | Europe | |
43943 | urine of a 12-year-old patient suffering from acute cystitis | 2015-04-15 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Disease | |
#Host Body Product | #Fluids | #Urine |
#Infection | #Patient |
taxonmaps
- @ref: 69479
- File name: preview.99_1698.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_247;96_965;97_1124;98_1340;99_1698&stattab=map
- Last taxonomy: Actinobaculum massiliense subclade
- 16S sequence: LN870313
- Sequence Identity:
- Total samples: 1977
- soil counts: 31
- aquatic counts: 21
- animal counts: 1924
- plant counts: 1
Safety information
risk assessment
- @ref: 23870
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 23870
- description: Actinobaculum massiliense partial 16S rRNA gene, strain FC3
- accession: LN870313
- length: 1501
- database: ena
- NCBI tax ID: 202789
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Actinobaculum massiliense FC3 | GCA_001457435 | scaffold | ncbi | 202789 |
66792 | Actinobaculum massiliense FC3 | 2811995073 | draft | img | 202789 |
GC content
- @ref: 23870
- GC-content: 60.17
- method: sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 96.838 | yes |
gram-positive | yes | 92.513 | no |
anaerobic | yes | 80.443 | no |
aerobic | no | 93.209 | yes |
halophile | no | 72.107 | no |
spore-forming | no | 96.23 | yes |
glucose-util | yes | 87.15 | no |
motile | no | 94.25 | yes |
thermophile | no | 95.379 | no |
glucose-ferment | yes | 71.676 | no |
External links
@ref: 23870
culture collection no.: DSM 100580, CSUR P1982
literature
- topic: Phylogeny
- Pubmed-ID: 27117391
- title: Description of strain FC3(T) as the neotype strain of Actinobaculum massiliense.
- authors: Bakour S, Beye M, Raoult D, Fournier PE
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001110
- year: 2016
- mesh: Actinomycetaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Child, Cystitis/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Humans, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Pathogenicity
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
23870 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100580 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100580) | |||
43943 | Sofiane Bakour, Mamadou Beye, Didier Raoult, Pierre-Edouard Fournier | Description of strain FC3T as the neotype strain of Actinobaculum massiliense | 10.1099/ijsem.0.001110 | IJSEM 66: 2702-2703 2016 | 27117391 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
68380 | Automatically annotated from API rID32A | |||||
69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |